Upgrade zarr-python dependency to 3.0 #275
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| **self._create_compressor_options(chunks), | ||
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| img_arr[...] = data |
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This breakage seems unintended from upstream discussion. We can revert after zarr-developers/zarr-python#2819 is released.
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We still have which looks like an internal issue in tifffile. Two more (both variants of
There are likely references to the NGFF version that don't handle "0.5" or have it as an option. That needs tests. |
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Thanks @aliddell! I believe the tifffile error is due to how zarr changed its interface to implement third-party storage types. We either need to wait for cgohlke/tifffile#282 or change the way we implement OME-TIFF support. However I think it's a relatively self-contained issue, and as long as the OME-Zarr part is migrated, we can continue to work on bridging acquire-zarr and iohub via Zarr v3/OME-Zarr v0.5. |
* use fsspec as a wrapper for ZarrTiffStore * update deprecated readers and tests * document the helper function * add back the binary check after a flag * use kwarg for file mode in reader * restore dtype attribute * restore opening zarr with dask * stringify path name * remove redundant dtype
it doesn't matter what the order is
this is not related to ome-zarr-py
| >>> new_plate = Plate.from_positions("combined.zarr", fovs) | ||
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| # TODO: remove when zarr-python adds back `copy_store` | ||
| raise NotImplementedError( |
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Blocked by upstream regression zarr-developers/zarr-python#2407
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We will use a dev branch for now to contain the user-facing changes given the upstream constraints.
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